Anopheles albimanus vs Anopheles dirus LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles dirus (Anopheles dirus, AdirW1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release . Anopheles albimanus was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 108,603

Genome coverage (bp) Coding exon coverage (bp)
Anopheles albimanus

Uncovered: 135,754,694 out of 173,339,240
Covered: 37,584,546 out of 173,339,240

Uncovered: 1,661,340 out of 20,837,397
Matches: 14,097,724 out of 20,837,397
Mismatches: 4,364,949 out of 20,837,397
Insertions: 713,384 out of 20,837,397

Anopheles dirus

Uncovered: 178,999,759 out of 216,307,690
Covered: 37,307,931 out of 216,307,690

Uncovered: 1,867,798 out of 21,020,835
Matches: 14,200,774 out of 21,020,835
Mismatches: 4,442,106 out of 21,020,835
Insertions: 510,157 out of 21,020,835

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Anopheles albimanus Anopheles dirus
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}